Fires in flight are acknowledged to be amongst the (if not the very) worst possible emergencies in an airliner (ignoring major structural failure).
In this case it has been reported that the fire was on the ground after disembarkation of passengers and occurred some time after starting the APU.
Suppressing and finally extinguishing the resulting fire presented a significant challenge to presumably well-equipped ground-based rescue and fire personnel.
Initial reports indicate that the fire was extinguished about 40 minutes after arrival of the first rescue and fire personnel.
A time of 40 minutes for ground personnel to contain and extinguish the fire does not give anyone a "warm fuzzy" feeling.
The APU battery is not accessible to the crew in-flight and so if it caught fire in-flight after the APU was started, only the aircraft fire indications, aircraft fire suppression/extinguishing systems could be used. This immediately brings into sharp focus exactly what is the capability of the inbuilt aircraft fire fighting systems in the case of a APU Battery fire?
Therefore the JAL APU Battery fire incident/accident would seem to qualify as a critical flight safety issue for the Boeing B787.
The "easy" workaround would seem to be to disable the APU battery and associated systems inflight, until an acceptable fix can be implemented.
But, nothing in aviation ever seems to be easy...and the Boeing/FAA political decisions based on sound engineering data and recommendations that need to be taken in this case will have to get it exactly correct.